interfaces.camino2trackvis.convert

Camino2Trackvis

Link to code

Wraps command camino_to_trackvis

Wraps camino_to_trackvis from Camino-Trackvis

Convert files from camino .Bfloat format to trackvis .trk format.

Example

>>> import nipype.interfaces.camino2trackvis as cam2trk
>>> c2t = cam2trk.Camino2Trackvis()
>>> c2t.inputs.in_file = 'data.Bfloat'
>>> c2t.inputs.out_file = 'streamlines.trk'
>>> c2t.inputs.min_length = 30
>>> c2t.inputs.data_dims = [128, 104, 64]
>>> c2t.inputs.voxel_dims = [2.0, 2.0, 2.0]
>>> c2t.inputs.voxel_order = 'LAS'
>>> c2t.run()                  

Inputs:

[Mandatory]
data_dims: (a list of from 3 to 3 items which are an integer (int or
         long))
        Three comma-separated integers giving the number of voxels along
        each dimension of the source scans.
        flag: -d %s, position: 4
in_file: (an existing file name)
        The input .Bfloat (camino) file.
        flag: -i %s, position: 1
voxel_dims: (a list of from 3 to 3 items which are a float)
        Three comma-separated numbers giving the size of each voxel in mm.
        flag: -x %s, position: 5
voxel_order: (a file name)
        Set the order in which various directions were stored. Specify with
        three letters consisting of one each from the pairs LR, AP, and SI.
        These stand for Left-Right, Anterior-Posterior, and Superior-
        Inferior. Whichever is specified in each position will be the
        direction of increasing order. Read coordinate system from a NIfTI
        file.
        flag: --voxel-order %s, position: 6

[Optional]
args: (a unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
min_length: (a float)
        The minimum length of tracts to output
        flag: -l %d, position: 3
nifti_file: (an existing file name)
        Read coordinate system from a NIfTI file.
        flag: --nifti %s, position: 7
out_file: (a file name)
        The filename to which to write the .trk (trackvis) file.
        flag: -o %s, position: 2
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

trackvis: (an existing file name)
        The filename to which to write the .trk (trackvis) file.

Trackvis2Camino

Link to code

Wraps command trackvis_to_camino

Inputs:

[Mandatory]
in_file: (an existing file name)
        The input .trk (trackvis) file.
        flag: -i %s, position: 1

[Optional]
append_file: (an existing file name)
        A file to which the append the .Bfloat data.
        flag: -a %s, position: 2
args: (a unicode string)
        Additional parameters to the command
        flag: %s
environ: (a dictionary with keys which are a newbytes or None or a
         newstr or None and with values which are a newbytes or None or a
         newstr or None, nipype default value: {})
        Environment variables
ignore_exception: (a boolean, nipype default value: False)
        Print an error message instead of throwing an exception in case the
        interface fails to run
out_file: (a file name)
        The filename to which to write the .Bfloat (camino).
        flag: -o %s, position: 2
terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
        Control terminal output: `stream` - displays to terminal immediately
        (default), `allatonce` - waits till command is finished to display
        output, `file` - writes output to file, `none` - output is ignored

Outputs:

camino: (an existing file name)
        The filename to which to write the .Bfloat (camino).